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<head> 
<title>PDB2PQR Server</title>
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<BODY>
<h2>PDB2PQR Server</h2>
<P>
<I>Currently using PDB2PQR Version 1.7.1</I>
<P>
Return to <a href="http://www.poissonboltzmann.org/pdb2pqr">the PDB2PQR homepage</a>.<br> 	
<hr> 	
This server enables a user to convert <a href="http://www.rcsb.org/pdb/">PDB</a> files into PQR files.  PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius.<P>

pKa calculations are performed by <a href="http://propka.ki.ku.dk">PROPKA</a>.<P>

For more information on PDB2PQR please see the:<BR>
<ul>
	<li> <a href="http://www.poissonboltzmann.org/pdb2pqr">Home Page</a>
	</li>
	<li> <a href="http://pdb2pqr.sourceforge.net/userguide.html">User Guide</a> </li>
	<li> <a href="http://pdb2pqr.sourceforge.net/examples/">Examples</a> </li>
</ul>

If you use the PDB2PQR service in a publication, please cite:
<blockquote>Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. <I>Nucleic Acids Research</I> <B>32</B> W665-W667 (2004). [<a href="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_2/W665">Link</a>]
</blockquote>

<hr>
<B>Note:</B> In order to distribute server load, the PDB2PQR server currently
is limited to a maximum size of 10000 atoms per protein.  If you are interested
in using PDB2PQR for larger proteins, you are encouraged to download a command
line version of PDB2PQR from the <a
	href="http://www.poissonboltzmann.org/pdb2pqr">PDB2PQR home page</a>.  For
additional limitations, please see the <a
	href="http://pdb2pqr.sourceforge.net/userguide.html">PDB2PQR user
	guide</a> <P>
<B>Note:</B> This server uses automatic refreshing to update the status of your PDB2PQR submission.  Do not use the <i>back</i> button on your browser while the server is running.<P>

<FORM action="http://linnetMINT/pdb2pqr/pdb2pqr.cgi" METHOD="POST" ENCTYPE="multipart/form-data" name="thisform">

Please enter either:
<blockquote>
<input type="RADIO" name="PDBSOURCE" value="ID" onClick="check(this.value)" CHECKED>a PDB ID</input>: <input type="text" name="PDBID" size=4 maxlength=6 value=""> <BR>
<input type="RADIO" name="PDBSOURCE" value="UPLOAD" onClick="check(this.value)">upload a PDB file</input>: <input type="file" name="PDB" size="25" maxlength=100 value="" DISABLED>
</blockquote>
<P>

Pick a forcefield to use: 
<blockquote>
<input type="RADIO" name="FF" id = "amber" value="amber" onClick="setff(this.value)">AMBER</input><BR> 
<input type="RADIO" name="FF" id = "charmm" value="charmm" onClick="setff(this.value)">CHARMM</input><BR>
<input type="RADIO" name="FF" id = "parse" value="parse" onClick="setff(this.value)" CHECKED >PARSE</input><BR>
<input type="RADIO" name="FF" id = "peoepb" value="peoepb" onClick="setff(this.value)">PEOEPB</input><BR>
<input type="RADIO" name="FF" id = "swanson" value="swanson" onClick="setff(this.value)">SWANSON</input><BR> 
<input type="RADIO" name="FF" id = "tyl06" value="tyl06" onClick="setff(this.value)">TYL06</input><BR>
<input type="RADIO" name="FF" id = "user" value="user" onClick="setff(this.value)">User-defined forcefield (<a href="http://pdb2pqr.sourceforge.net/userguide.html#userff">help</a>): <input type="file" name="USERFF" size="25" maxlength=100 value="" DISABLED><BR>
<label>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;User-defined names (<a href="http://pdb2pqr.sourceforge.net/userguide.html#userff">help</a>):</label> <input type="file" name="USERNAMES" size="25" maxlength=100 value="" DISABLED><BR>
<label>&nbsp;&nbsp;* If you select user-defined forcefield, you also need to specify a user-defined .names file.</label><BR> 
</blockquote>

Pick an output naming scheme to use (<a href="http://pdb2pqr.sourceforge.net/userguide.html#outff">help</a>):
<blockquote>
<input type="RADIO" name="FFOUT" value="internal" CHECKED>Internal naming scheme</input> (<a href="http://pdb2pqr.sourceforge.net/programmerguide.html#canon">What's this?</a>)<BR>
<input type="RADIO" name="FFOUT" value="amber">AMBER</input><BR>
<input type="RADIO" name="FFOUT" value="charmm">CHARMM</input><BR>
<input type="RADIO" name="FFOUT" value="parse">PARSE</input><BR>
<input type="RADIO" name="FFOUT" value="peoepb">PEOEPB</input><BR>
<input type="RADIO" name="FFOUT" value="swanson">SWANSON</input><BR>
<input type="RADIO" name="FFOUT" value="tyl06">TYL06</input>

</blockquote>

Available options: 
<blockquote>
<input type="CHECKBOX" name="DEBUMP" CHECKED> Ensure that new atoms are not rebuilt too close to existing atoms<BR>
<input type="CHECKBOX" name="OPT" CHECKED onClick="setwatopt()"> Optimize the hydrogen bonding network<BR>
<input type="CHECKBOX" name="PROPKA" value="SETPKA" onClick="setph(this.value)"> Use <a href="http://propka.ki.ku.dk">PROPKA</a> to assign protonation states at pH <input type="text" name="PH" size=4 maxlength=6  value="7" DISABLED><BR>
<input type="CHECKBOX" name="LIGANDCHECK" onClick="setligand()"> Assign charges to the ligand specified in a MOL2 file</input>: <input type="file" name="LIGAND" size="25" maxlength=100 value="" DISABLED><BR>
<input type="CHECKBOX" name="INPUT" CHECKED> Create an <a href="http://apbs.wustl.edu">APBS</a> input file <span style="font-size:60%">(this also enables the option to run APBS and visualize your results through the web interface, if it has been installed)</span><BR>
<input type="CHECKBOX" name="CHAIN"> Add/keep chain IDs in the PQR file<BR>
<input type="CHECKBOX" name="WHITESPACE"> Insert whitespaces between atom name and residue name, between x and y, and between y and z<BR>
<input type="CHECKBOX" name="TYPEMAP"> Create Typemap output<BR>
<input type="CHECKBOX" name="NEUTRALN" onClick="setneutraln()"> Make the protein's N-terminus neutral (requires PARSE forcefield)<BR>
<input type="CHECKBOX" name="NEUTRALC" onClick="setneutralc()"> Make the protein's C-terminus neutral (requires PARSE forcefield)
</blockquote>

<input type="submit" value="Submit"><P>
</form> 
<HR>
The PDB2PQR application and web server was written by:
<blockquote>
<a href="http://enzyme.ucd.ie//group_members/jens/">Jens Erik Nielsen</a><BR>
<a href="http://agave.wustl.edu">Todd Dolinsky</a><BR>
<a href="http://agave.wustl.edu">Nathan Baker</a><P>
</blockquote>
PDB2PQR Opal integration by:
<blockquote>
<a href="http://nbcr.net">Wes Goodman</a><BR>
<a href="http://agave.wustl.edu">Samir Unni</a><BR>
<a href="http://agave.wustl.edu">Yong Huang</a><P>
</blockquote>
JMol visualization scripts and applets provided by:
<blockquote>
<a href="http://chemapps.stolaf.edu/jmol">Robert Hanson</a><P>
</blockquote>

PDB2PQR is supported by NIH grant GM069702-01 to NAB, the NPACI Alpha Project program, and the <a href="http://nbcr.net">National Biomedical Computation Resource</a>.<P>

Before sending a bug report you may want to check the <a href="http://sourceforge.net/mailarchive/forum.php?forum=pdb2pqr-users">pdb2pqr-users mailing list archives</a> or the existing <a href="http://sourceforge.net/tracker/?group_id=144228&atid=758143">PDB2PQR SourceForge Bug List</a> to make sure your question has not already been addressed. Otherwise please post all bug reports or feature requests to the appropriate <a href="http://sourceforge.net/tracker/?group_id=144228">PDB2PQR SourceForge Tracker</a>.<P>
For additional support you may contact the <a href="http://lists.sourceforge.net/lists/listinfo/pdb2pqr-users">pdb2pqr-users mailing list</a>.<P>
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